Hydrophilic labels for biomolecules

A biocompatible dye composition comprising at least one excipient and an isolated enantiomeric mixture selected from

• diastereomer Ia,
• diastereomer Ib,
• diastereomer IIa,
• or, diastereomer IIb,
• whereby diastereomers Ia and Ib are derived from general formula I
• and diastereomers IIa and IIb are derived from general formula II,
• and whereby each of R1 and R2 is the same or different and is independently selected from the group consisting of an aliphatic and heteroaliphatic group;
• each of L1 to L4 is the same or different and is independently selected from the group consisting of a divalent linear (—(CH2)o—, o=1 to 15), crossed, or cyclic alkylene group which can be substituted by at least one atom selected from the group consisting of oxygen, substituted nitrogen, and sulfur;
• X1 is selected from the group consisting of —OH, —SH, —NH2, —NH—NH2, —F, —Cl, —Br, —I, —NHS (hydroxysuccinimidyl/sulfosuccinimidyl), —O-STP (4-sulfo-2,3,5,6-tetrafluorophenoxy), —O-TFP (2,3,5,6-tetrafluorophenoxy), —O-benzotriazole, -benzotriazole, —NR-L-OH, —NR-L-O-phosphoramidite, —NR-L-SH, —NR-L-NH2, —NR-L-NH—NH2, —NR-L-CO2H, —NR-L-CO2—NHS, —NR-L-CO2—STP, —NR-L-CO2-TFP, —NR-L-CO-benzotriazole, —NR-L-CHO, —NR-L-maleimid, and —NR-L-NH—CO—CH2—I, R is —H or is equal to R1 or R2′ and L is equal to L1 to L4;
• each of X2 and X3 is the same or different and is independently selected from the group consisting of hydrogen, alkyl-, tert-alkyl-, aryl-, carboxyaryl-, dicarboxyaryl-, heteroaryl-, cycloalkyl-, heterocycloalkyl-, alkyloxy-, alkylmercapto-, aryloxy, arylmercapto, hydroxy-, amino-, nitro-, and cyano-residues, or is a solubilizing or ionizable substituent selected from the group consisting of —SO3−, —PO32−, —CO2−, tert-ammonium, cyclodextrine, sugar, and combinations thereof;
• Kat is a number of Na+, K+, Ca2+, ammonia, or other cation(s) needed to compensate the negative charge brought by the cyanine;
• n in formula I is a integer from 0 to 3;
• Y in formula II is selected from the group consisting of fluorine, chlorine, bromine, a substituted phenoxy-, and a substituted arylmercapto-(phenyl sulfanyl-) function;
• and
• each of R3 and R4 in formula II is the same or different and is independently an aliphatic or heteroaliphatic group respectively, or forms together the divalent structural element selected from the group consisting of —(CH2)m—, —(CH2)mO(CH2)m′—, —(CH2)mS(CH2)m′—, —(CH2)mCH═CH—, and —OCH═CH— where each of m and m′ is the same or different and is a integer from 2 to 6.

A method of labeling at least one biomolecule, the method comprising

• providing a composition comprising at least one excipient and one isolated enantiomeric mixture in an effective concentration to at least one biomolecule under conditions sufficient for binding the enantiomeric mixture to the biomolecule, and detecting the biomolecule-bound enantiomeric mixture,
• where the one isolated enantiomeric mixture is
• diastereomer Ia
• diastereomer Ib
• diastereomer IIa,
• or, diastereomer IIb,
• whereby diastereomers Ia and Ib are derived from general formula I
• and diastereomers IIa and IIb are derived from general formula II,
• and whereby
• each of R1 and R2 is the same or different and is independently selected from the group consisting of an aliphatic and heteroaliphatic group;
• each of L1 to L4 is the same or different and is independently selected from the group consisting of a divalent linear (—(CH2)o—, o=1 to 15), crossed, or cyclic alkylene group which can be substituted by at least one atom selected from the group consisting of oxygen, substituted nitrogen, and sulfur;
• X1 is selected from the group consisting of —OH, —SH, —NH2, —NH—NH2, —F, —Cl, —Br, —I, —NHS (hydroxysuccinimidyl/sulfosuccinimidyl), —O-STP (4-sulfo-2,3,5,6-tetrafluorophenoxy), —O-TFP (2,3,5,6-tetrafluorophenoxy), —O-benzotriazole, -benzotriazole, —NR-L-OH, —NR-L-O-phosphoramidite, —NR-L-SH, —NR-L-NH2, —NR-L-NH—NH2, —NR-L-CO2H, —NR-L-CO2—NHS, —NR-L-CO2—STP, —NR-L-CO2-TFP, —NR-L-CO-benzotriazole, —NR-L-CHO, —NR-L-maleimid, and —NR-L-NH—CO—CH2—I, R is —H or is equal to R1 or R2′ and L is equal to L1 to L4;
• each of X2 and X3 is the same or different and is independently selected from the group consisting of hydrogen, alkyl-, tert-alkyl-, aryl-, carboxyaryl-, dicarboxyaryl-, heteroaryl-, cycloalkyl-, heterocycloalkyl-, alkyloxy-, alkylmercapto-, aryloxy, arylmercapto, hydroxy-, amino-, nitro-, and cyano-residues, or is a solubilizing or ionizable substituent selected from the group consisting of —SO3−, —PO32−, —CO2−, tert-ammonium, cyclodextrine, sugar, and combinations thereof;
• Kat is a number of Na+, K+, Ca2+, ammonia, or other cation(s) needed to compensate the negative charge brought by the cyanine;
• n in formula I is a integer from 0 to 3;
• Y in formula II is selected from the group consisting of fluorine, chlorine, bromine, a substituted phenoxy-, and a substituted arylmercapto-(phenyl sulfanyl-) function;
• and
• each of R3 and R4 in formula II is the same or different and is independently an aliphatic or heteroaliphatic group respectively, or forms together the divalent structural element selected from the group consisting of —(CH2)m—, —(CH2)mO(CH2)m′—, —(CH2)mS(CH2)m′—, —(CH2)mCH═CH—, and —OCH═CH— where each of m and m′ is the same or different and is a integer from 2 to 6.